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JAL-3148 further bug fix to state of 'colourBy'
[jalview.git]
/
src
/
jalview
/
schemes
/
ResidueProperties.java
diff --git
a/src/jalview/schemes/ResidueProperties.java
b/src/jalview/schemes/ResidueProperties.java
index
55df1d1
..
a4e6480
100755
(executable)
--- a/
src/jalview/schemes/ResidueProperties.java
+++ b/
src/jalview/schemes/ResidueProperties.java
@@
-39,14
+39,14
@@
public class ResidueProperties
public static final int[] purinepyrimidineIndex;
public static final int[] purinepyrimidineIndex;
- public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
+ public static final Map<String, Integer> aa3Hash = new HashMap<>();
- public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
+ public static final Map<String, String> aa2Triplet = new HashMap<>();
- public static final Map<String, String> nucleotideName = new HashMap<String, String>();
+ public static final Map<String, String> nucleotideName = new HashMap<>();
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
- public static final Map<String, String> modifications = new HashMap<String, String>();
+ public static final Map<String, String> modifications = new HashMap<>();
static
{
static
{
@@
-496,25
+496,27
@@
public class ResidueProperties
* Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
*/
* Color.white, // R Color.white, // Y Color.white, // N Color.white, // Gap
*/
- public static List<String> STOP = Arrays.asList("TGA", "TAA", "TAG");
+ public static String STOP = "STOP";
+
+ public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG");
public static String START = "ATG";
/**
* Nucleotide Ambiguity Codes
*/
public static String START = "ATG";
/**
* Nucleotide Ambiguity Codes
*/
- public static final Map<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+ public static final Map<String, String[]> ambiguityCodes = new Hashtable<>();
/**
* Codon triplets with additional symbols for unambiguous codons that include
* ambiguity codes
*/
/**
* Codon triplets with additional symbols for unambiguous codons that include
* ambiguity codes
*/
- public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+ public static final Hashtable<String, String> codonHash2 = new Hashtable<>();
/**
* all ambiguity codes for a given base
*/
/**
* all ambiguity codes for a given base
*/
- public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
+ public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<>();
static
{
static
{
@@
-638,7
+640,7
@@
public class ResidueProperties
List<String> codesfor = _ambiguityCodes.get(r);
if (codesfor == null)
{
List<String> codesfor = _ambiguityCodes.get(r);
if (codesfor == null)
{
- _ambiguityCodes.put(r, codesfor = new ArrayList<String>());
+ _ambiguityCodes.put(r, codesfor = new ArrayList<>());
}
if (!codesfor.contains(acode.getKey()))
{
}
if (!codesfor.contains(acode.getKey()))
{
@@
-755,27
+757,27
@@
public class ResidueProperties
}
// Stores residue codes/names and colours and other things
}
// Stores residue codes/names and colours and other things
- public static Map<String, Map<String, Integer>> propHash = new Hashtable<String, Map<String, Integer>>();
+ public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
- public static Map<String, Integer> hydrophobic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> hydrophobic = new Hashtable<>();
- public static Map<String, Integer> polar = new Hashtable<String, Integer>();
+ public static Map<String, Integer> polar = new Hashtable<>();
- public static Map<String, Integer> small = new Hashtable<String, Integer>();
+ public static Map<String, Integer> small = new Hashtable<>();
- public static Map<String, Integer> positive = new Hashtable<String, Integer>();
+ public static Map<String, Integer> positive = new Hashtable<>();
- public static Map<String, Integer> negative = new Hashtable<String, Integer>();
+ public static Map<String, Integer> negative = new Hashtable<>();
- public static Map<String, Integer> charged = new Hashtable<String, Integer>();
+ public static Map<String, Integer> charged = new Hashtable<>();
- public static Map<String, Integer> aromatic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> aromatic = new Hashtable<>();
- public static Map<String, Integer> aliphatic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> aliphatic = new Hashtable<>();
- public static Map<String, Integer> tiny = new Hashtable<String, Integer>();
+ public static Map<String, Integer> tiny = new Hashtable<>();
- public static Map<String, Integer> proline = new Hashtable<String, Integer>();
+ public static Map<String, Integer> proline = new Hashtable<>();
static
{
static
{
@@
-1149,7
+1151,7
@@
public class ResidueProperties
String cdn = codonHash2.get(lccodon.toUpperCase());
if ("*".equals(cdn))
{
String cdn = codonHash2.get(lccodon.toUpperCase());
if ("*".equals(cdn))
{
- return "STOP";
+ return STOP;
}
return cdn;
}
}
return cdn;
}
@@
-1157,7
+1159,7
@@
public class ResidueProperties
public static Hashtable<String, String> toDssp3State;
static
{
public static Hashtable<String, String> toDssp3State;
static
{
- toDssp3State = new Hashtable<String, String>();
+ toDssp3State = new Hashtable<>();
toDssp3State.put("H", "H");
toDssp3State.put("E", "E");
toDssp3State.put("C", " ");
toDssp3State.put("H", "H");
toDssp3State.put("E", "E");
toDssp3State.put("C", " ");
@@
-2525,7
+2527,7
@@
public class ResidueProperties
// / cut here
public static void main(String[] args)
{
// / cut here
public static void main(String[] args)
{
- Hashtable<String, Vector<String>> aaProps = new Hashtable<String, Vector<String>>();
+ Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
System.out.println("my %aa = {");
// invert property hashes
for (String pname : propHash.keySet())
System.out.println("my %aa = {");
// invert property hashes
for (String pname : propHash.keySet())
@@
-2536,7
+2538,7
@@
public class ResidueProperties
Vector<String> aprops = aaProps.get(rname);
if (aprops == null)
{
Vector<String> aprops = aaProps.get(rname);
if (aprops == null)
{
- aprops = new Vector<String>();
+ aprops = new Vector<>();
aaProps.put(rname, aprops);
}
Integer hasprop = phash.get(rname);
aaProps.put(rname, aprops);
}
Integer hasprop = phash.get(rname);
@@
-2578,7
+2580,7
@@
public class ResidueProperties
public static List<String> getResidues(boolean forNucleotide,
boolean includeAmbiguous)
{
public static List<String> getResidues(boolean forNucleotide,
boolean includeAmbiguous)
{
- List<String> result = new ArrayList<String>();
+ List<String> result = new ArrayList<>();
if (forNucleotide)
{
for (String nuc : nucleotideName.keySet())
if (forNucleotide)
{
for (String nuc : nucleotideName.keySet())